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With many of President Bush’s tax cuts set to expire within the next two years, Barack Obama’s historic ascendancy to the presidency could have major implications for the corporate tax structure. But tax experts still puzzle over exactly what they are. That’s because — except in a few areas, such as his opposition to tax breaks for oil companies — business taxes were not a focal point of the Obama campaign, and the president-elect has done little in his formal platform to clarify matters.

“There will be a waiting game here before we see a lot of details,” Lindy Paull, partner in PricewaterhouseCoopers’ national tax services group, tells CFO.com. Paull, a former chief of staff of the Congressional Joint Committee on Taxation, joins other experts when she suggests that corporations generally should not expect big tax hits, either through a higher corporate tax rate or otherwise. Members of Congress are sensitive to the U.S. corporate tax rate being steeper than in most other countries, she says — “a concern if you’re thinking about competitiveness in the world marketplace.”

Other revenue-raising tax initiatives that Sen. Obama mentioned in his campaign may also get shut down. Sen. Obama is “coming into a very fragile economy, and will probably have to rethink the reality of what he would like to do,” says Paul Beecy, tax partner with Grant Thornton, and leader of its transaction advisory tax services practice. He’s “got to step back and realize this is a negotiated process, even among members of your own party.”

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As for the specifics that Sen. Obama has offered, certain industries would benefit through his promise to make the research-and-development credit permanent, and to support alternative energy projects. Others — especially oil and gas companies, of course — could be in for sharp reductions in their current tax advantages. The candidate called out many of the special tax incentives that such companies now receive, and bills that seek to strip some incentives already are moving through the House of Representatives, says John Abernethy, a director with the federal income tax practice at Ryan, a tax advisory firm. “They’re making so much money, they’re easy targets,” Abernethy says.

Of concern for multinational companies could be the campaign promise to shut down the current policy that allows companies to defer paying taxes on overseas earnings until they are repatriated “to end the incentive for companies to ship jobs overseas.” Says Lindy Paull, “From the standpoint of multinational companies, deferral isn’t what causes them to ship jobs overseas — a lot of goods that go into the market need to be produced nearby.” Still, no one is sounding alarm bells yet, since so few details have emerged.

Other items in Sen. Obama’s platform leave the experts scratching their heads.

The president-elect, for example, has vowed to crack down on “offshore pension loopholes,” a phrase that remains mysterious to Abernethy. “I just don’t know what they’re talking about. Nobody tried to offer that to me when I was in industry,” even when he was vice president of tax for an energy company that moved its headquarters offshore, he says.

Paull expects the first impact on corporate taxes to come through an economic stimulus package that Congress is expected to try passing during its lame-duck session later this month. That package could contain tax incentives like a business tax credit for new hires, and increased small-business expensing limits, Paull says, based on her conversations with congressional staffers. It could also extend some of the tax incentives from the stimulus package passed earlier this year, including a “bonus” depreciation that lets companies write off more upfront, and an expansion of the treatment of net operating losses, so that more companies could qualify for a tax refund.

The first real clues to a more comprehensive policy should come in February or March, when President Obama submits his first budget to Congress. But even then, he will be able to defer some decisions. Major items like the current 15-percent rate for capital gains and taxes on dividends aren’t set to rise until the end of 2010. “And that’s where it will get interesting,” says Paull. “It’s going to be a challenge to extend those.”

One salve for companies may be in the sensibilities of Sen. Obama’s own economic training and associations from the University of Chicago, Harvard, and elsewhere. Abernethy notes that his chief economic advisor during his campaign, UC professor Austan Goolsbee, published a paper in 2006 showing how taxes on broadband Internet technology would have hampered its spread. “At least one person on the team understands that if you tax something too hard, it goes away,” he says.